If you really want beautiful scenery & nature trails/hiking, you would be better to do Rishiri-Rebun-Sarobetsu National Park (NP), Shiretoko NP, and Akan NP, or spend four days per one NP in your two weeks. You could add Daisetsuzan NP and set three days per NP, or exchange Rishiri and Daisetsuzan, based on their geological locations. Anyway, Shiretoko and Akan should remain in the final list.
https://www.env.go.jp/en/nature/nps/park/parks/index.htmlhttps://www.env.go.jp/en/nature/nps/park/rishiri/guide/view.htmlhttps://www.env.go.jp/en/nature/nps/park/shiretoko/guide/view.htmlhttps://www.env.go.jp/en/nature/nps/park/akan/guide/view.htmlhttps://www.env.go.jp/en/nature/nps/park/daisetsu/guide/view.htmlRebun island is known to a paradise of trekking.
http://www.rebun-island.jp/en/trekking/index.htmlHowever, it would not likely that sunny days last for all the two weeks. It would be better to do cities on rainy days. The top cities in Hokkaido would be Hakodate and Sapporo. So, the best combination would be Shiretoko, Akan, Hakodate, and Sapporo. Book flights to/from Chitose. Just before you start the travel, check the weather forecasts for the next two weeks. If sunny days were in the first week, do Shiretoko and Akan first. If in the second week, do Hakodate and Sapporo first. If in the middle, do Hakodate, then Shiretoko and Akan, and Sapporo at the last. If rainy days were in the middle, you would have to split Shiretoko and Akan.
Adopt a similar strategy, in the case you choose five destinations with three days each. I mean Hakodate, Sapporo, Shiretoko, Akan, and Daisetsuzan/Furano.
It would better to utilize public transportations for long distance moves. Airplanes and express trains would be faster than cars. You could have a rest on highway buses. Try to use your energy just for driving in the destination areas.
If you really want to do all by your own driving, then just give up the treasures in Hokkaido. You could easily fill up other substitutes in your itinerary. They might not be the best grade, but still very good ones. See Google ratings for those; most are four stars and above.
Hakodate
- Onuma Park
https://www.google.co.jp/maps/place/大沼国定公園/@41.9817318,140.6720396,12z
- Ota Shrine
https://www.google.co.jp/maps/place/太田神社（拝殿）/@42.2540866,139.7531929,12z/
- Cape Chikyu
https://www.google.co.jp/maps/place/地球岬/@42.3017516,140.9996231,12z/
- Lake Kuttara
https://www.google.co.jp/maps/place/倶多楽湖/@42.4999084,141.1644109,12z
- Lake Shikotsu
https://www.google.co.jp/maps/place/支笏湖/@42.7728402,141.4025597,12z
- Lake Toya
https://www.google.co.jp/maps/place/洞爺湖/@42.5626318,140.817048,12z
- Fukidashi Park
https://www.google.co.jp/maps/place/ふきだし公園/@42.8581639,140.8686737,12z
- Cape Kamui
https://www.google.co.jp/maps/place/神威岬展望台/@43.333645,140.3456059,12z
- Cape Shakotan
https://www.google.co.jp/maps/place/積丹岬/@43.3712367,140.4624569,12z
- Shimamui Coast
https://www.google.co.jp/maps/place/島武意海岸/@43.3741032,140.4785729,12z
- Cape Gold
https://www.google.co.jp/maps/place/黄金岬/@43.302458,140.6010479,12z
- Blue Cave
https://www.google.co.jp/maps/place/青い洞窟/@43.2141078,140.9262545,15z
- Takino Park
https://www.google.co.jp/maps/place/国営滝野すずらん丘陵公園/@42.9135046,141.3870073,15z
Blue Cave Tours are from Otaru
http://hokuo-marine.com/and from Shiriuchi near Hakodate.
http://www.854.jp/tour.phphttps://www.google.co.jp/maps/place/矢越クルーズ(矢越海岸アドベンチャーズのりば)/@41.5323667,140.4181379,17z
You could climb Komagatake with one hour from Onuma Park.
https://www.google.co.jp/maps/place/駒ケ岳/@42.0633333,140.6728112,14z
It would take one hour to climb Tarumaesan in Lake Shikoto.
https://www.google.co.jp/maps/place/樽前山/@42.6903324,141.3746105,13z/
80 minutes to climb Washibetsudake near Cape Chikyu.
https://www.google.co.jp/maps/place/鷲別岳/@42.435693,141.000987,14z
Shioyamaruyama in Otaru is an easy mountain.
https://www.google.co.jp/maps/place/塩谷丸山/@43.179036,140.9225855,17z
Hakkenzan near Jozankei in one hour.
Iwaonupuri in Niseko in 100 min.
https://www.google.co.jp/maps/place/イワオヌプリ/@42.8866451,140.6383744,14z/
Shinsennuma in Niseko has hiking trails.
http://www.town.kyowa.hokkaido.jp/kankou/spot/files/sinsennumaenglish....https://www.google.co.jp/maps/place/神仙沼自然休養林展望台/@42.9042388,140.5906567,16z
Here are counterparts in Shiretoko, Akan, and Daisetsuzan areas.
--- Shiretoko
Kamuiwakka Falls
https://www.google.co.jp/maps/place/カムイワッカの滝/@44.1588539,145.1222327,15z
Shiretoko Five Lakes
https://www.google.co.jp/maps/place/知床五湖フィールドハウス/@44.1222118,145.080396,15z
Flepe Falls
https://www.google.co.jp/maps/place/flepe+waterfall+フレペの滝/@44.0966198,145.0118306,17z/
Cape Puyuni
https://www.google.co.jp/maps/place/プユニ岬/@44.0950276,145.0092406,15z
The Road to the Heaven
https://www.google.co.jp/maps/place/天に続く道/@43.9061968,144.7761583,15z
Shiretoko Pass
https://www.google.co.jp/maps/place/知床峠パーキング/@44.0542268,145.104729,15z
Lake Rausu
https://www.google.co.jp/maps/place/羅臼湖/@44.0326956,145.0781097,16z
Rausu Onsen
https://www.google.co.jp/maps/place/羅臼温泉+熊の湯/@44.03196,145.1554478,15z
Aidomari Onsen
https://www.google.co.jp/maps/place/相泊温泉/@44.1845635,145.3173619,15z
--- Shiretoko-Akan
Milk Road
https://www.google.co.jp/maps/place/北19号/@43.6081041,144.8791003,15z/
Kaiyodai
https://www.google.co.jp/maps/place/開陽台/@43.613918,144.8702101,15z
Yoroushi Onsen
https://www.google.co.jp/maps/place/湯宿だいいち/@43.5875682,144.7225703,15z
Cherry Falls
https://www.google.co.jp/maps/place/さくらの滝/@43.7318761,144.5230607,16z
Kaminoko Pond
https://www.google.co.jp/maps/place/神の子池/@43.6452506,144.5479632,17z
--- Akan
Lake Mashu
https://www.google.co.jp/maps/place/摩周第三展望台/@43.583105,144.4950496,15z
Kawayu Onsen
https://www.google.co.jp/maps/place/川湯温泉駅/@43.616267,144.457662,15z/
Atosanupuri
https://www.google.co.jp/maps/place/硫黄山/@43.6101943,144.4364066,15z
Kotan Onsen
https://www.google.co.jp/maps/place/コタン温泉露天風呂/@43.5647321,144.3413323,15z
Bihoro Pass
https://www.google.co.jp/maps/place/美幌峠展望台/@43.6453139,144.2485506,15z
Tsubetsu Pass
https://www.google.co.jp/maps/place/津別峠展望施設/@43.5773726,144.2240501,15z
Meruhen Hill
https://www.google.co.jp/maps/place/ビューポイントパーキング+女満別「メルヘンの丘」/@43.9225803,144.1904672,15z
Tawadaira
https://www.google.co.jp/maps/place/%E5%A4%9A%E5%92%8C%E5%B9%B3%E5%B1%...The 900 Field
https://www.google.co.jp/maps/place/９００草原/@43.4557951,144.448562,17z
Lake Akan
https://www.google.co.jp/maps/place/阿寒湖/@43.4344499,144.0991741,17z
Akanko Onsen
https://www.google.co.jp/maps/place/阿寒湖温泉/@43.4341662,144.0869977,16z
Lake Onnetoh
https://www.google.co.jp/maps/place/オンネトー湖/@43.384614,143.9655489,16z
--- Daisetsuzan
Taushubetsu Bridge
https://www.google.co.jp/maps/place/タウシュベツ川橋梁/@43.415497,143.1894245,15z
Naitai Kogen Bokujo
https://www.google.co.jp/maps/place/ナイタイ+高原牧場/@43.2858934,143.1143308,12z
Kogen Onsen
https://www.google.co.jp/maps/place/高原温泉/@43.6262955,142.9310542,15z
Soukyo
https://www.google.co.jp/maps/place/層雲峡/@43.7213016,142.9606767,14z
Ryusei Ginga Falls
https://www.google.co.jp/maps/place/流星・銀河の滝/@43.7213016,142.9694314,15z
Shujitsu Hill
https://www.google.co.jp/maps/place/就実の丘/@43.6304849,142.4969972,15z
Jetcoaster Road
https://www.google.co.jp/maps/place/ジェットコースターの路/@43.5114522,142.422402,15z
Tokachidake Bogakudai
https://www.google.co.jp/maps/place/十勝岳望岳台/@43.4460725,142.6479752,17z
You could climb Kurodake for about 1-1.5 hours.
https://www.google.co.jp/maps/place/黒岳/@43.6983318,142.9194457,17z
Asahidake needs 2.5 hours.
https://www.google.co.jp/maps/place/旭岳/@43.6636111,142.8519779,14z
Ginsendai Hiking Trails
http://www.town.hokkaido-kamikawa.lg.jp/section/sangyoukeizai/chs81200...https://www.google.co.jp/maps/place/銀泉台/@43.6708331,142.9606733,16z
Kogen Onsen Hiking Trails
http://www.town.hokkaido-kamikawa.lg.jp/section/sangyoukeizai/chs81200...
